joshsbloom
commented
4 years ago Hi Harshil,
We've been using an R-based pipeline at UCLA. Also been working on a conda environment to automate setup of everything except bcl2fastq (see attached files). Will update that on ucla swabseq git repo as soon as I can.
Highly recommend however that you use the kallisto/bustools framework that Sina has developed. It is especially helpful for nextseq/miniseq runs where the per base error rate is higher. It is nicely made and has little dependencies, so not much need for containers there.
Best, Josh
On 8/27/20 8:16 AM, Harshil Patel wrote:
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Hi @joshsbloomhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_joshsbloom&d=DwMFaQ&c=UXmaowRpu5bLSLEQRunJ2z-YIUZuUoa9Rw_x449Hd_Y&r=L8-RAUDUpAyb0fNSb4_w7vt4L_MZrMlN6wK0EL4LuFU&m=LJvIdNoOry8i-Ke38KaeECXJUJF1zIBghkHf2MSyAXU&s=kE7bOsp78YRabuHqW9X3OdoXFJg1NTVkXnEFc2uau90&e= @sbooeshaghihttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_sbooeshaghi&d=DwMFaQ&c=UXmaowRpu5bLSLEQRunJ2z-YIUZuUoa9Rw_x449Hd_Y&r=L8-RAUDUpAyb0fNSb4_w7vt4L_MZrMlN6wK0EL4LuFU&m=LJvIdNoOry8i-Ke38KaeECXJUJF1zIBghkHf2MSyAXU&s=mYfJcYOoheSRRF5gmBkgXTLwO15VUWK2kFSFGGZNUcg&e=! Hope you and loved ones are doing well during these difficult times.
Firstly, I would like to thank you and everyone else involved in the development of this versatile and high-throughput assay. Truly amazing! I am a bioinformatician working at The Francis Crick Institute in London, and our first set of Swab-Seq samples are being sequenced as we speak. I sat down today to collate a list of resources and to bring myself up-to-speed on how to perform the downstream analysis (listed below just in case it benefits anyone else):
Swab-Seq GitHub repo - @octantbiohttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_octantbio_SwabSeq&d=DwMFaQ&c=UXmaowRpu5bLSLEQRunJ2z-YIUZuUoa9Rw_x449Hd_Y&r=L8-RAUDUpAyb0fNSb4_w7vt4L_MZrMlN6wK0EL4LuFU&m=LJvIdNoOry8i-Ke38KaeECXJUJF1zIBghkHf2MSyAXU&s=xlt65iwbWtNczxKeQZP9pCEpw18ysb1D-S_2sLCuc5Y&e= Swab-Seq GitHub repo - @joshsbloomhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_joshsbloom_swabseq&d=DwMFaQ&c=UXmaowRpu5bLSLEQRunJ2z-YIUZuUoa9Rw_x449Hd_Y&r=L8-RAUDUpAyb0fNSb4_w7vt4L_MZrMlN6wK0EL4LuFU&m=LJvIdNoOry8i-Ke38KaeECXJUJF1zIBghkHf2MSyAXU&s=KqIQaSbS2qn3rj-aS_B42NXgpFi-CwaVUeSU_lLnK4U&e=
Kallisto/bustools pre-print @sbooeshaghihttps://urldefense.proofpoint.com/v2/url?u=https-3A__www.medrxiv.org_content_10.1101_2020.05.13.20100131v1&d=DwMFaQ&c=UXmaowRpu5bLSLEQRunJ2z-YIUZuUoa9Rw_x449Hd_Y&r=L8-RAUDUpAyb0fNSb4_w7vt4L_MZrMlN6wK0EL4LuFU&m=LJvIdNoOry8i-Ke38KaeECXJUJF1zIBghkHf2MSyAXU&s=vhUtClyG9bRf_UhBABr_DoLqEAr6ZKxT_7tUC66Aaes&e= Kallisto/bustools pre-print GitHub repo - @pachterlabhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_pachterlab_BLCSBGLKP-5F2020&d=DwMFaQ&c=UXmaowRpu5bLSLEQRunJ2z-YIUZuUoa9Rw_x449Hd_Y&r=L8-RAUDUpAyb0fNSb4_w7vt4L_MZrMlN6wK0EL4LuFU&m=LJvIdNoOry8i-Ke38KaeECXJUJF1zIBghkHf2MSyAXU&s=eN1aU88kStuNQf4Ihl2Y8tCy0tnp-sfjrqdvGTNBKjQ&e=
I should also say that I am one of the core contributors to the nf-core frameworkhttps://urldefense.proofpoint.com/v2/url?u=https-3A__nf-2Dco.re_&d=DwMFaQ&c=UXmaowRpu5bLSLEQRunJ2z-YIUZuUoa9Rw_x449Hd_Y&r=L8-RAUDUpAyb0fNSb4_w7vt4L_MZrMlN6wK0EL4LuFU&m=LJvIdNoOry8i-Ke38KaeECXJUJF1zIBghkHf2MSyAXU&s=5BFKifWEq86n_wAsz2_lf2C-h2MwOmSu59_wdL-2Eh8&e= and I was recently involved in writing an end-to-end pipeline to perform assembly and intra-host/low-frequency variant calling for viral samples sequenced on the Illumina platform - nf-core/viralreconhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_nf-2Dcore_viralrecon&d=DwMFaQ&c=UXmaowRpu5bLSLEQRunJ2z-YIUZuUoa9Rw_x449Hd_Y&r=L8-RAUDUpAyb0fNSb4_w7vt4L_MZrMlN6wK0EL4LuFU&m=LJvIdNoOry8i-Ke38KaeECXJUJF1zIBghkHf2MSyAXU&s=1ht6MzXjCtP9owqkm9Ec6i7X7W4HJmdLp9Fqbnnuono&e=.
- Would I be correct in assuming that this repo contains the most up-to-date analysis scripts for Swab-seq?
- Are you using software containers for the analysis? I couldn't see a Dockerfile or any other pointers.
- Would this pipeline and the bioinformatics community as a whole benefit from it being added to nf-core? I haven't actually run it from end-to-end and I'd rather not assume anything especially since I have seen some scripts that point to more interactive methods of analysis using Jupyter notebooks / Rstudio đ
Thanks in advance!
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drpatelh
Hi @joshsbloom @sbooeshaghi! Hope you and loved ones are doing well during these difficult times.
Firstly, I would like to thank you and everyone else involved in the development of this versatile and high-throughput assay. Truly amazing! I am a bioinformatician working at The Francis Crick Institute in London, and our first set of Swab-Seq samples are being sequenced as we speak. I sat down today to collate a list of resources and to bring myself up-to-speed on how to perform the downstream analysis (listed below just in case it benefits anyone else):
Swab-Seq pre-print
Swab-Seq GitHub repo - @octantbio Swab-Seq GitHub repo - @joshsbloom
Kallisto/bustools pre-print @sbooeshaghi Kallisto/bustools pre-print GitHub repo - @pachterlab
Sri Kosuri Talk on 23/07/20
Octant Notion link
I should also say that I am one of the core contributors to the nf-core framework and I was recently involved in writing an end-to-end pipeline to perform assembly and intra-host/low-frequency variant calling for viral samples sequenced on the Illumina platform - nf-core/viralrecon.
Dockerfileor any other pointers.Thanks in advance!